Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010517.1 Kokia drynarioides strain JFW-HI SEQ_125429, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 220654
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 203 characters in sequence are not A, C, G, or T
Found at i:332 original size:4 final size:4
Alignment explanation
Indices: 312--397 Score: 68
Period size: 4 Copynumber: 21.2 Consensus size: 4
302 AACATATTAC
* * **
312 CTTT CTTT CCTT C-TT CTTT CTTT CCTCT CCAT C-TT CTTT CTTT CTTCT
1 CTTT CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT CTT-T
* * *
360 CCTT CTTC CTTT CTTT CCTT CTTTT CTTT CTTT CTTT C
1 CTTT CTTT CTTT CTTT CTTT C-TTT CTTT CTTT CTTT C
398 CCGTTTATTT
Statistics
Matches: 66, Mismatches: 11, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
3 5 0.08
4 52 0.79
5 9 0.14
ACGTcount: A:0.01, C:0.35, G:0.00, T:0.64
Consensus pattern (4 bp):
CTTT
Found at i:364 original size:17 final size:17
Alignment explanation
Indices: 312--391 Score: 76
Period size: 17 Copynumber: 4.6 Consensus size: 17
302 AACATATTAC
*
312 CTTTCTTTC--CTTCTT
1 CTTTCTTTCTTCTCCTT
*
327 CTTTCTTTCCTCTCCATCTT
1 CTTTCTTTCTTCT-C--CTT
347 CTTTCTTTCTTCTCCTT
1 CTTTCTTTCTTCTCCTT
*
364 CTTCCTTTCTT-TCCTT
1 CTTTCTTTCTTCTCCTT
380 CTTTTCTTTCTT
1 C-TTTCTTTCTT
392 TCTTTCCCGT
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
15 9 0.16
16 6 0.11
17 24 0.44
19 1 0.02
20 15 0.27
ACGTcount: A:0.01, C:0.35, G:0.00, T:0.64
Consensus pattern (17 bp):
CTTTCTTTCTTCTCCTT
Found at i:365 original size:13 final size:12
Alignment explanation
Indices: 314--398 Score: 57
Period size: 13 Copynumber: 7.0 Consensus size: 12
304 CATATTACCT
*
314 TTCTTTCCTT-C
1 TTCTTTCTTTCC
325 TTCTTTCTTTCC
1 TTCTTTCTTTCC
** *
337 TCTCCATC-TTCT
1 T-TCTTTCTTTCC
349 TTCTTTCTTCTCC
1 TTCTTTCTT-TCC
* *
362 TTCTTCCTTTCT
1 TTCTTTCTTTCC
* *
374 TTCCTTCTTTTCT
1 TTCTTTC-TTTCC
387 TTCTTTCTTTCC
1 TTCTTTCTTTCC
399 CGTTTATTTG
Statistics
Matches: 56, Mismatches: 13, Indels: 9
0.72 0.17 0.12
Matches are distributed among these distances:
11 13 0.23
12 18 0.32
13 25 0.45
ACGTcount: A:0.01, C:0.35, G:0.00, T:0.64
Consensus pattern (12 bp):
TTCTTTCTTTCC
Found at i:392 original size:17 final size:19
Alignment explanation
Indices: 312--398 Score: 106
Period size: 20 Copynumber: 4.5 Consensus size: 19
302 AACATATTAC
312 CTTTCTTTCCTTCTTCTTT
1 CTTTCTTTCCTTCTTCTTT
* *
331 CTTTCCTCTCCATCTTCTTT
1 CTTT-CTTTCCTTCTTCTTT
351 CTTTCTTCTCCTTCTTCCTTT
1 CTTTCTT-TCCTTCTT-CTTT
*
372 CTTTCCTT-CTT-TTCTTT
1 CTTTCTTTCCTTCTTCTTT
389 CTTTCTTTCC
1 CTTTCTTTCC
399 CGTTTATTTG
Statistics
Matches: 58, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
17 11 0.19
18 3 0.05
19 9 0.16
20 25 0.43
21 10 0.17
ACGTcount: A:0.01, C:0.36, G:0.00, T:0.63
Consensus pattern (19 bp):
CTTTCTTTCCTTCTTCTTT
Found at i:1083 original size:26 final size:25
Alignment explanation
Indices: 1031--1084 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 25
1021 TAAGTACAAA
*
1031 AAAACTTTTTAATATTTTATAGTACT
1 AAAACTTTTTAACATTTTATAG-ACT
1057 AAAACTTTATTAACATTTATATA-ACT
1 AAAACTTT-TTAACATTT-TATAGACT
1083 AA
1 AA
1085 TAGAATGATC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 13 0.52
27 8 0.32
28 4 0.16
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.44
Consensus pattern (25 bp):
AAAACTTTTTAACATTTTATAGACT
Found at i:16697 original size:2 final size:2
Alignment explanation
Indices: 16692--16727 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
16682 CATTGACAAA
16692 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16728 TAAAGGTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21243 original size:2 final size:2
Alignment explanation
Indices: 21238--21277 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
21228 TCAAGCATCA
21238 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
21278 GTATGCTGGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:34791 original size:17 final size:16
Alignment explanation
Indices: 34769--34800 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
34759 TATAATTATC
34769 TTTTTATTTTGTTAATA
1 TTTTTATTTT-TTAATA
34786 TTTTTATTTTTTAAT
1 TTTTTATTTTTTAAT
34801 CTCAAATCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (16 bp):
TTTTTATTTTTTAATA
Found at i:49555 original size:24 final size:26
Alignment explanation
Indices: 49507--49556 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
49497 TAAAGGTATT
49507 AAGTGGCAGCACTGTAAGAGGATTTTA
1 AAGTGGCAGCAC-GTAAGAGGATTTTA
49534 AAGTGGCAGCAC-T-AGAGGATTTT
1 AAGTGGCAGCACGTAAGAGGATTTT
49557 TTGCCACTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 10 0.43
25 1 0.04
27 12 0.52
ACGTcount: A:0.32, C:0.12, G:0.30, T:0.26
Consensus pattern (26 bp):
AAGTGGCAGCACGTAAGAGGATTTTA
Found at i:49827 original size:11 final size:11
Alignment explanation
Indices: 49793--49827 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
49783 TATATATAAT
49793 TTTATAAAAAAA
1 TTTAT-AAAAAA
*
49805 CTTATAAAAAA
1 TTTATAAAAAA
49816 TTTATAAAAAA
1 TTTATAAAAAA
49827 T
1 T
49828 ATTCCACCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 17 0.81
12 4 0.19
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (11 bp):
TTTATAAAAAA
Found at i:67241 original size:26 final size:26
Alignment explanation
Indices: 67212--67267 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
67202 GATGATAATG
67212 AATTTGGATATTTGT-AATTT-TTGTAA
1 AATTT-GA-ATTTGTAAATTTATTGTAA
*
67238 AATTTGAATTTGTAAATTTATTTTAA
1 AATTTGAATTTGTAAATTTATTGTAA
67264 AATT
1 AATT
67268 CAAATTCATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 6 0.22
25 7 0.26
26 14 0.52
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.54
Consensus pattern (26 bp):
AATTTGAATTTGTAAATTTATTGTAA
Found at i:67273 original size:26 final size:24
Alignment explanation
Indices: 67221--67273 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 24
67211 GAATTTGGAT
**
67221 ATTTGTAATTTTTGTAAAATTTGA
1 ATTTGTAATTTTTGTAAAATTCAA
*
67245 ATTTGTAAATTTATTTTAAAATTCAA
1 ATTTGT-AATTT-TTGTAAAATTCAA
67271 ATT
1 ATT
67274 CATATATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 6 0.25
25 5 0.21
26 13 0.54
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.53
Consensus pattern (24 bp):
ATTTGTAATTTTTGTAAAATTCAA
Found at i:74154 original size:55 final size:54
Alignment explanation
Indices: 74053--74162 Score: 150
Period size: 55 Copynumber: 2.0 Consensus size: 54
74043 ATTAAAAAGT
*
74053 AGTTTGAAAGAGAAGTTTGTTTATAGTAATAACTTTATACGTTTGTTGAATTAAG
1 AGTTTGAAAGAGAAGTTTGTTTATAGTAATAACTTTATA-GGTTGTTGAATTAAG
* * *
74108 AGTTTGAAAGAGAAGTTTTTTTATGGTAATAACATTTGAT-GGTTGTTTAATTAAG
1 AGTTTGAAAGAGAAGTTTGTTTATAGTAATAAC-TTT-ATAGGTTGTTGAATTAAG
74163 TATTATGGTA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
55 44 0.90
56 3 0.06
57 2 0.04
ACGTcount: A:0.34, C:0.03, G:0.21, T:0.43
Consensus pattern (54 bp):
AGTTTGAAAGAGAAGTTTGTTTATAGTAATAACTTTATAGGTTGTTGAATTAAG
Found at i:91535 original size:2 final size:2
Alignment explanation
Indices: 91528--91552 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
91518 CAGGAAGAGC
91528 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
91553 GGAGCACTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:91663 original size:3 final size:3
Alignment explanation
Indices: 91655--91689 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
91645 ATGATTTGGA
*
91655 GGT GGT GGT GGT GGT GGT GGT GGA GGT GGT GGT GG
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GG
91690 GAGACTGCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.03, C:0.00, G:0.69, T:0.29
Consensus pattern (3 bp):
GGT
Found at i:98140 original size:1 final size:1
Alignment explanation
Indices: 98106--98132 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
98096 NNNNNNNNNN
98106 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
98133 CTCTTTTTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:106238 original size:11 final size:11
Alignment explanation
Indices: 106222--106250 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
106212 AATGGGGGGC
106222 TTTAAGGGTTT
1 TTTAAGGGTTT
106233 TTTAAGGGTTT
1 TTTAAGGGTTT
106244 TTTAAGG
1 TTTAAGG
106251 TAGCAAAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.21, C:0.00, G:0.28, T:0.52
Consensus pattern (11 bp):
TTTAAGGGTTT
Found at i:109257 original size:6 final size:6
Alignment explanation
Indices: 109246--109274 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
109236 ATTTTTTTTT
109246 GTTTCC GTTTCC GTTTCC GTTTCC GTTTC
1 GTTTCC GTTTCC GTTTCC GTTTCC GTTTC
109275 GAAATTCTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.17, T:0.52
Consensus pattern (6 bp):
GTTTCC
Found at i:118752 original size:28 final size:27
Alignment explanation
Indices: 118721--118774 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 27
118711 AAAATAAATA
118721 TAAA-TTATTTAAAATATTAAAATTATGT
1 TAAAGTTATTTAAAATA--AAAATTATGT
*
118749 TAAATGTTTTTTAAAATAAAAATTAT
1 TAAA-GTTATTTAAAATAAAAATTAT
118775 AAATAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
28 12 0.52
30 11 0.48
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (27 bp):
TAAAGTTATTTAAAATAAAAATTATGT
Found at i:120694 original size:14 final size:14
Alignment explanation
Indices: 120661--120708 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
120651 AATATAAAAA
*
120661 ATTTTAAAATATATT
1 ATTTTAAAAT-TTTT
120676 A-TTTAAAATTTTT
1 ATTTTAAAATTTTT
*
120689 ATTTTAAACTTTTT
1 ATTTTAAAATTTTT
120703 -TTTTAA
1 ATTTTAA
120709 TTTTTCGTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 10 0.33
14 19 0.63
15 1 0.03
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (14 bp):
ATTTTAAAATTTTT
Found at i:120953 original size:20 final size:19
Alignment explanation
Indices: 120930--120993 Score: 53
Period size: 20 Copynumber: 3.4 Consensus size: 19
120920 TATTGTTAAC
120930 AAATTTAATTTATATAAACA
1 AAATTTAATTTAT-TAAACA
* * *
120950 AAATTTTA-TTGTT-GAC-
1 AAATTTAATTTATTAAACA
*
120966 AAATTTAATTAATTTAAACA
1 AAATTTAATTTA-TTAAACA
120986 AAATTTAA
1 AAATTTAA
120994 ACACAATAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 8
0.69 0.15 0.17
Matches are distributed among these distances:
16 7 0.21
17 3 0.09
18 3 0.09
19 5 0.15
20 15 0.45
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (19 bp):
AAATTTAATTTATTAAACA
Found at i:120959 original size:36 final size:36
Alignment explanation
Indices: 120919--120991 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
120909 TTTAATTATA
*
120919 TTATTGTTAACAAATTTAATTTATATAAACAAAATT
1 TTATTGTTAACAAATTTAATTAATATAAACAAAATT
* *
120955 TTATTGTTGACAAATTTAATTAATTTAAACAAAATT
1 TTATTGTTAACAAATTTAATTAATATAAACAAAATT
120991 T
1 T
120992 AAACACAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.45
Consensus pattern (36 bp):
TTATTGTTAACAAATTTAATTAATATAAACAAAATT
Found at i:124109 original size:30 final size:31
Alignment explanation
Indices: 124075--124132 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
124065 CAACCCAATA
124075 ACTTAAATAAAAAC-TTCAAATAGTTTAGTG
1 ACTTAAATAAAAACTTTCAAATAGTTTAGTG
* *
124105 ACTTAAATGAAAACTTTCAAATATTTTA
1 ACTTAAATAAAAACTTTCAAATAGTTTA
124133 ATGATTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 13 0.52
31 12 0.48
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.36
Consensus pattern (31 bp):
ACTTAAATAAAAACTTTCAAATAGTTTAGTG
Found at i:124948 original size:4 final size:4
Alignment explanation
Indices: 124926--124964 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
124916 ACAAATTAAC
* *
124926 AAAT GAAT AAAT GAAAT AAAT AAAT ACAT AAAT AAAT AA
1 AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AA
124965 TAACAAGAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
4 26 0.87
5 4 0.13
ACGTcount: A:0.69, C:0.03, G:0.05, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:133398 original size:176 final size:176
Alignment explanation
Indices: 133104--133456 Score: 706
Period size: 176 Copynumber: 2.0 Consensus size: 176
133094 TACACAAGAT
133104 TTTCAATTATCAATGTCTGGGTCTTGAGCTTATAGACACAGACAACCCAAATTGATGTTAATTGG
1 TTTCAATTATCAATGTCTGGGTCTTGAGCTTATAGACACAGACAACCCAAATTGATGTTAATTGG
133169 TAATTGTCTAAAAAAAGAAAATTGGGTATGGGCCTACATGCATGTAATAAAAGATTCATACAAAT
66 TAATTGTCTAAAAAAAGAAAATTGGGTATGGGCCTACATGCATGTAATAAAAGATTCATACAAAT
133234 CGTTTACTTGCATATATAAACTAAGGTCAATTAATTTTATGATTGA
131 CGTTTACTTGCATATATAAACTAAGGTCAATTAATTTTATGATTGA
133280 TTTCAATTATCAATGTCTGGGTCTTGAGCTTATAGACACAGACAACCCAAATTGATGTTAATTGG
1 TTTCAATTATCAATGTCTGGGTCTTGAGCTTATAGACACAGACAACCCAAATTGATGTTAATTGG
133345 TAATTGTCTAAAAAAAGAAAATTGGGTATGGGCCTACATGCATGTAATAAAAGATTCATACAAAT
66 TAATTGTCTAAAAAAAGAAAATTGGGTATGGGCCTACATGCATGTAATAAAAGATTCATACAAAT
133410 CGTTTACTTGCATATATAAACTAAGGTCAATTAATTTTATGATTGA
131 CGTTTACTTGCATATATAAACTAAGGTCAATTAATTTTATGATTGA
133456 T
1 T
133457 ATTCTAATAG
Statistics
Matches: 177, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
176 177 1.00
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (176 bp):
TTTCAATTATCAATGTCTGGGTCTTGAGCTTATAGACACAGACAACCCAAATTGATGTTAATTGG
TAATTGTCTAAAAAAAGAAAATTGGGTATGGGCCTACATGCATGTAATAAAAGATTCATACAAAT
CGTTTACTTGCATATATAAACTAAGGTCAATTAATTTTATGATTGA
Found at i:142469 original size:59 final size:59
Alignment explanation
Indices: 142366--142517 Score: 173
Period size: 59 Copynumber: 2.6 Consensus size: 59
142356 GAGACCCCTA
* * *
142366 TTTATCTGATAAAAAAATTAAATTTTTGGGTGTTGGCTACGCAATAG-CCGACACCCTTTT
1 TTTATCAGAT-AAAAAATTAAATTTTTTGGTGTTAGCTACGCAAT-GTCCGACACCCTTTT
* * * * * *
142426 TTTATTAGATAAAAATTTTAATTTTTTGGTGTTAGTTATGCAATGTCCGACATCCTTTT
1 TTTATCAGATAAAAAATTAAATTTTTTGGTGTTAGCTACGCAATGTCCGACACCCTTTT
*
142485 TTTATCAGATAAAAAA-TACAATTTTTTTGTGTT
1 TTTATCAGATAAAAAATTA-AATTTTTTGGTGTT
142518 GGCCATACAA
Statistics
Matches: 77, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
58 2 0.03
59 67 0.87
60 8 0.10
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (59 bp):
TTTATCAGATAAAAAATTAAATTTTTTGGTGTTAGCTACGCAATGTCCGACACCCTTTT
Found at i:142529 original size:59 final size:58
Alignment explanation
Indices: 142366--142583 Score: 166
Period size: 59 Copynumber: 3.7 Consensus size: 58
142356 GAGACCCCTA
* * ** * ** *
142366 TTTATCTGATAAAAAAATTAAATTTTTGGGTGTTGGCTACGCAATAGCCGACACCCTTTT
1 TTTATCAGAT-AAAAAATTCAATTTTTTTGTGTTGGCCATACAATGGCCGACA-CCTTTT
* * * * * ** * *
142426 TTTATTAGATAAAAATTTTAATTTTTTGGTGTTAGTTATGCAATGTCCGACATCCTTTT
1 TTTATCAGATAAAAAATTCAATTTTTTTGTGTTGGCCATACAATGGCCGACA-CCTTTT
* ** ** *
142485 TTTATCAGATAAAAAATACAATTTTTTTGTGTTGGCCATACAATGGCTAACACCCCTA
1 TTTATCAGATAAAAAATTCAATTTTTTTGTGTTGGCCATACAATGGCCGACACCTTTT
*
142543 TTTATCTGATAAAAAATTTCAAATTTTTTTGGTGTTGGCCA
1 TTTATCAGATAAAAAA-TTC-AATTTTTTT-GTGTTGGCCA
142584 CAAATTTTTA
Statistics
Matches: 127, Mismatches: 28, Indels: 5
0.79 0.17 0.03
Matches are distributed among these distances:
58 18 0.14
59 82 0.65
60 17 0.13
61 10 0.08
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.41
Consensus pattern (58 bp):
TTTATCAGATAAAAAATTCAATTTTTTTGTGTTGGCCATACAATGGCCGACACCTTTT
Found at i:154125 original size:31 final size:31
Alignment explanation
Indices: 154090--154148 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
154080 TGGTACAATA
* *
154090 TATACCTGAAGTTCTAATTGTGATTTAAATG
1 TATACCTAAAATTCTAATTGTGATTTAAATG
* * *
154121 TATACTTAAAATTTTAATTTTGATTTAA
1 TATACCTAAAATTCTAATTGTGATTTAA
154149 TCATACACAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 23 1.00
ACGTcount: A:0.36, C:0.07, G:0.10, T:0.47
Consensus pattern (31 bp):
TATACCTAAAATTCTAATTGTGATTTAAATG
Found at i:169035 original size:29 final size:29
Alignment explanation
Indices: 168978--169035 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
168968 AGTTGGTATC
* *
168978 TGTAATTTTATACATAAATTTTGATTTTG
1 TGTAATTTTATACATAAAATTTGAATTTG
*
169007 TGTAATTTTATATATAAAAATTT-AATTTG
1 TGTAATTTTATACAT-AAAATTTGAATTTG
169036 ATTTAAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 19 0.76
30 6 0.24
ACGTcount: A:0.36, C:0.02, G:0.09, T:0.53
Consensus pattern (29 bp):
TGTAATTTTATACATAAAATTTGAATTTG
Found at i:169733 original size:30 final size:31
Alignment explanation
Indices: 169699--169767 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
169689 CATTTAACAC
*
169699 AACAGTCACTCAAC-TT-T-GAAAATGTGACAA
1 AACAGTCACT-AACATTATCGAAAA-GTGAAAA
169729 AACAGTCACTAACATTATCGAAAAGTGAAAA
1 AACAGTCACTAACATTATCGAAAAGTGAAAA
169760 AACAGTCA
1 AACAGTCA
169768 TTGATAAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
29 3 0.09
30 12 0.34
31 15 0.43
32 5 0.14
ACGTcount: A:0.48, C:0.19, G:0.13, T:0.20
Consensus pattern (31 bp):
AACAGTCACTAACATTATCGAAAAGTGAAAA
Found at i:170750 original size:30 final size:31
Alignment explanation
Indices: 170683--170753 Score: 94
Period size: 31 Copynumber: 2.3 Consensus size: 31
170673 CCATAATTTC
170683 AGTGACTGTTTTGTCACTTTTCGATAACGTT
1 AGTGACTGTTTTGTCACTTTTCGATAACGTT
*
170714 AGTGACTTTTTTGTCACATTTTC-A-AA-GTT
1 AGTGACTGTTTTGTCAC-TTTTCGATAACGTT
170743 AAGTGACTGTT
1 -AGTGACTGTT
170754 GTGTAATGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
29 3 0.08
30 11 0.31
31 17 0.47
32 5 0.14
ACGTcount: A:0.23, C:0.14, G:0.18, T:0.45
Consensus pattern (31 bp):
AGTGACTGTTTTGTCACTTTTCGATAACGTT
Found at i:178598 original size:15 final size:15
Alignment explanation
Indices: 178580--178638 Score: 57
Period size: 15 Copynumber: 3.8 Consensus size: 15
178570 AACAAAAATT
178580 ACAACAAAAACAGTA
1 ACAACAAAAACAGTA
178595 ACAA-AAATAACAGTAAA
1 ACAACAAA-AACAGT--A
* *
178612 ACAACAAAAAAAATA
1 ACAACAAAAACAGTA
*
178627 ACAGCAAAAACA
1 ACAACAAAAACA
178639 ACAAAAATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 3 0.08
15 21 0.58
17 9 0.25
18 3 0.08
ACGTcount: A:0.71, C:0.17, G:0.05, T:0.07
Consensus pattern (15 bp):
ACAACAAAAACAGTA
Found at i:178647 original size:21 final size:21
Alignment explanation
Indices: 178553--178677 Score: 101
Period size: 21 Copynumber: 5.7 Consensus size: 21
178543 AAAAAGCATA
**
178553 AAAAATAACA-CTCAAACAAC
1 AAAAATAACAGCAAAAACAAC
* *
178573 AAAAATTACAACAAAAACAGTAAC
1 AAAAATAACAGCAAAAAC---AAC
* *
178597 AAAAATAACAGTAAAACAACAAA
1 AAAAATAACAG-CAAA-AACAAC
178620 AAAAATAACAGCAAAAACAAC
1 AAAAATAACAGCAAAAACAAC
*
178641 AAAAATAATAGCAAAAACAGCACC
1 AAAAATAACAGCAAAAACA--A-C
178665 AAAAA-AACAGCAA
1 AAAAATAACAGCAA
178678 TATATTTTTT
Statistics
Matches: 85, Mismatches: 11, Indels: 15
0.77 0.10 0.14
Matches are distributed among these distances:
20 9 0.11
21 28 0.33
22 3 0.04
23 21 0.25
24 18 0.21
25 3 0.04
26 3 0.04
ACGTcount: A:0.69, C:0.18, G:0.05, T:0.08
Consensus pattern (21 bp):
AAAAATAACAGCAAAAACAAC
Found at i:178674 original size:44 final size:44
Alignment explanation
Indices: 178594--178677 Score: 107
Period size: 44 Copynumber: 1.9 Consensus size: 44
178584 CAAAAACAGT
*
178594 AACAAAAATAACAGTAAAACAACAAAAAAAATAACAGCAAAAAC
1 AACAAAAATAACAGAAAAACAACAAAAAAAATAACAGCAAAAAC
* * **
178638 AACAAAAATAATAGCAAAAACAGCACCAAAAA-AACAGCAA
1 AACAAAAATAACAG-AAAAACAACAAAAAAAATAACAGCAA
178678 TATATTTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 21 0.62
45 13 0.38
ACGTcount: A:0.70, C:0.18, G:0.06, T:0.06
Consensus pattern (44 bp):
AACAAAAATAACAGAAAAACAACAAAAAAAATAACAGCAAAAAC
Found at i:178676 original size:23 final size:24
Alignment explanation
Indices: 178569--178677 Score: 111
Period size: 23 Copynumber: 4.8 Consensus size: 24
178559 AACACTCAAA
* *
178569 CAACAAAAATTACAACAAAAACAG
1 CAACAAAAATAACAGCAAAAACAG
* * *
178593 TAACAAAAATAACAG-TAAAACAA
1 CAACAAAAATAACAGCAAAAACAG
*
178616 CAAAAAAAATAACAGC-AAAA-A-
1 CAACAAAAATAACAGCAAAAACAG
*
178637 CAACAAAAATAATAGCAAAAACAG
1 CAACAAAAATAACAGCAAAAACAG
*
178661 CACCAAAAA-AACAGCAA
1 CAACAAAAATAACAGCAA
178678 TATATTTTTT
Statistics
Matches: 70, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
21 14 0.20
22 5 0.07
23 31 0.44
24 20 0.29
ACGTcount: A:0.69, C:0.18, G:0.06, T:0.07
Consensus pattern (24 bp):
CAACAAAAATAACAGCAAAAACAG
Found at i:179998 original size:16 final size:15
Alignment explanation
Indices: 179958--179998 Score: 52
Period size: 13 Copynumber: 2.9 Consensus size: 15
179948 TTTCAACTTT
179958 ATTTT-AATAATAAA
1 ATTTTAAATAATAAA
179972 A-TTTAAA-AATAATA
1 ATTTTAAATAATAA-A
179986 ATTTTAAATAATA
1 ATTTTAAATAATA
179999 TTCTTTAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 8 0.35
14 5 0.22
15 6 0.26
16 4 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATTTTAAATAATAAA
Found at i:180051 original size:15 final size:15
Alignment explanation
Indices: 180031--180087 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
180021 ACTCAATATT
180031 AATATTTTAATAATA
1 AATATTTTAATAATA
*
180046 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
180065 AATATATTAATAATA
1 AATATTTTAATAATA
*
180080 AATGTTTT
1 AATATTTT
180088 GTAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:191323 original size:16 final size:16
Alignment explanation
Indices: 191302--191336 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
191292 TAAATTACTG
191302 ATTACAA-CTCTATTTT
1 ATTACAACCT-TATTTT
191318 ATTACAACCTTATTTT
1 ATTACAACCTTATTTT
191334 ATT
1 ATT
191337 CCTGCCATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.89
17 2 0.11
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTACAACCTTATTTT
Found at i:196858 original size:23 final size:23
Alignment explanation
Indices: 196821--196917 Score: 133
Period size: 23 Copynumber: 4.2 Consensus size: 23
196811 ACACTAGCAC
* *
196821 GCTCTCTGTTTAGCACGTTT-CGT
1 GCTCTCTGATTAGCAC-TTTGTGT
* *
196844 GCCCTCTGATCAGCACTTTGTGT
1 GCTCTCTGATTAGCACTTTGTGT
196867 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTTTGTGT
*
196890 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTTTGTGT
196913 GCTCT
1 GCTCT
196918 GTGTTACCCA
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
22 3 0.05
23 63 0.95
ACGTcount: A:0.11, C:0.26, G:0.23, T:0.40
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTTTGTGT
Found at i:201280 original size:5 final size:5
Alignment explanation
Indices: 201270--201294 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
201260 GCATATTTAC
201270 GGGGA GGGGA GGGGA GGGGA GGGGA
1 GGGGA GGGGA GGGGA GGGGA GGGGA
201295 ATTGCATTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.80, T:0.00
Consensus pattern (5 bp):
GGGGA
Found at i:203771 original size:164 final size:163
Alignment explanation
Indices: 203593--203924 Score: 592
Period size: 164 Copynumber: 2.0 Consensus size: 163
203583 AACAGCTGCT
*
203593 TAAGTCACACTCCTTGGAATCTATTGCTAGAATATACGTTCATTACTCATGGGATACCAAGTTTT
1 TAAGTCACACTCCTTGGAATCTATTGCTAGAATATACGTCCATTACTCATGGGATACCAAGTTTT
* *
203658 AATTTTTTTCCCCTAATCTGTTTCAATCCAGTTCTTTAGCAATGTTAGTGTACGTACTAGTAAAA
66 AATATTTTTCCCCTAATCTGTTTCAATCCAGTTCTTTAGCAATGTTAATGTACGTACTAGTAAAA
*
203723 GTTCTAGCGTTTTGCTAACTCATTCATGTTAAA
131 GTTCTAGCGTTTGGCTAACTCATTCATGTTAAA
* *
203756 TAAGTCCATACTCCTTGGAATCTATTGCTCGAATATACGTCCATTACTCATGGGATACCAAGTTT
1 TAAGT-CACACTCCTTGGAATCTATTGCTAGAATATACGTCCATTACTCATGGGATACCAAGTTT
203821 TAATATTTTTCCCCTAATCTGTTTCAATCCAGTTCTTTAGCAATGTTAATGTACGTACTAGTAAA
65 TAATATTTTTCCCCTAATCTGTTTCAATCCAGTTCTTTAGCAATGTTAATGTACGTACTAGTAAA
*
203886 AGTTCTAGCGTTTGGCTAACTTATTCATGTTAAA
130 AGTTCTAGCGTTTGGCTAACTCATTCATGTTAAA
203920 TAAGT
1 TAAGT
203925 TCTATGGTGC
Statistics
Matches: 161, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
163 5 0.03
164 156 0.97
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (163 bp):
TAAGTCACACTCCTTGGAATCTATTGCTAGAATATACGTCCATTACTCATGGGATACCAAGTTTT
AATATTTTTCCCCTAATCTGTTTCAATCCAGTTCTTTAGCAATGTTAATGTACGTACTAGTAAAA
GTTCTAGCGTTTGGCTAACTCATTCATGTTAAA
Found at i:206842 original size:98 final size:97
Alignment explanation
Indices: 206650--206844 Score: 354
Period size: 98 Copynumber: 2.0 Consensus size: 97
206640 AGCATTATCC
*
206650 TTATTGAAGAATATAAAGAAGATACGCTTGGAAACGTTGGAATAATTTTTTAGAAAAACTGAAAT
1 TTATTGAAGAATATAAAGAAGATAAGCTTGGAAACGTTGGAATAATTTTTTAGAAAAACTGAAAT
206715 TAAATTAAAGGCAAATTCACCTCGAAATCTAA
66 TAAATTAAAGGCAAATTCACCTCGAAATCTAA
*
206747 TTATTGAAGAATATAAAGAAGATAAGCTTGGAAACGTTGGTATAATTTTTTTAGAAAAACTGAAA
1 TTATTGAAGAATATAAAGAAGATAAGCTTGGAAACGTTGGAATAA-TTTTTTAGAAAAACTGAAA
*
206812 TTAAATTAAAGGCAAATTCACCTCGGAATCTAA
65 TTAAATTAAAGGCAAATTCACCTCGAAATCTAA
206845 GACAGGTTTA
Statistics
Matches: 94, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
97 43 0.46
98 51 0.54
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.30
Consensus pattern (97 bp):
TTATTGAAGAATATAAAGAAGATAAGCTTGGAAACGTTGGAATAATTTTTTAGAAAAACTGAAAT
TAAATTAAAGGCAAATTCACCTCGAAATCTAA
Found at i:209641 original size:7 final size:7
Alignment explanation
Indices: 209629--209655 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
209619 AAGGAGGTGA
209629 TTACCAG
1 TTACCAG
209636 TTACCAG
1 TTACCAG
209643 TTACCAG
1 TTACCAG
209650 TTACCA
1 TTACCA
209656 TGCTCTGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.30, G:0.11, T:0.30
Consensus pattern (7 bp):
TTACCAG
Found at i:211057 original size:31 final size:31
Alignment explanation
Indices: 210999--211059 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
210989 ATTTTTAATT
***
210999 TAATAATTATTTTCATTGTGGGGTTTGAATA
1 TAATAATTATTTTCATTGTGAAATTTGAATA
211030 TAATAATTATTTTCATAT-TGAAATTTGAAT
1 TAATAATTATTTTCAT-TGTGAAATTTGAAT
211060 TTTAAGACTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 25 0.96
32 1 0.04
ACGTcount: A:0.34, C:0.03, G:0.13, T:0.49
Consensus pattern (31 bp):
TAATAATTATTTTCATTGTGAAATTTGAATA
Found at i:215557 original size:21 final size:22
Alignment explanation
Indices: 215531--215578 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
215521 AATTGTTGCT
215531 TTTTTGTTGCTGTTTT-CATTG
1 TTTTTGTTGCTGTTTTCCATTG
*
215552 TTTTTGTTGTTGTTTTGCCATTG
1 TTTTTGTTGCTGTTTT-CCATTG
215575 TTTT
1 TTTT
215579 GGTATCGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 15 0.62
23 9 0.38
ACGTcount: A:0.04, C:0.08, G:0.19, T:0.69
Consensus pattern (22 bp):
TTTTTGTTGCTGTTTTCCATTG
Found at i:219499 original size:141 final size:141
Alignment explanation
Indices: 219245--219526 Score: 555
Period size: 141 Copynumber: 2.0 Consensus size: 141
219235 AGTTTAAAAA
219245 AGAGACATGATTTTAAGCTTCTATAGCTTTCTTAACTGATGGTATTTGGAATCTATAGTTTTCTG
1 AGAGACATGATTTTAAGCTTCTATAGCTTTCTTAACTGATGGTATTTGGAATCTATAGTTTTCTG
*
219310 AACCCAGTTGTAGATCCCAGGAGCTTACACTTGGTGGATGATACTGTGAAGAAGCTGCCAATATA
66 AACCCAGTTGTAGATCCCAGGAGCTTACACTTAGTGGATGATACTGTGAAGAAGCTGCCAATATA
219375 ATAATGGGTGT
131 ATAATGGGTGT
219386 AGAGACATGATTTTAAGCTTCTATAGCTTTCTTAACTGATGGTATTTGGAATCTATAGTTTTCTG
1 AGAGACATGATTTTAAGCTTCTATAGCTTTCTTAACTGATGGTATTTGGAATCTATAGTTTTCTG
219451 AACCCAGTTGTAGATCCCAGGAGCTTACACTTAGTGGATGATACTGTGAAGAAGCTGCCAATATA
66 AACCCAGTTGTAGATCCCAGGAGCTTACACTTAGTGGATGATACTGTGAAGAAGCTGCCAATATA
219516 ATAATGGGTGT
131 ATAATGGGTGT
219527 TTGTAAGGCC
Statistics
Matches: 140, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
141 140 1.00
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (141 bp):
AGAGACATGATTTTAAGCTTCTATAGCTTTCTTAACTGATGGTATTTGGAATCTATAGTTTTCTG
AACCCAGTTGTAGATCCCAGGAGCTTACACTTAGTGGATGATACTGTGAAGAAGCTGCCAATATA
ATAATGGGTGT
Found at i:220322 original size:19 final size:20
Alignment explanation
Indices: 220285--220324 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
220275 TGGATTTTTT
*
220285 TTTTTTTTTTAAATCATTAA
1 TTTTTTTTTAAAATCATTAA
220305 TTTTTTTTTAAAAT-ATTAA
1 TTTTTTTTTAAAATCATTAA
220324 T
1 T
220325 AATTTTTATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTTTTTTTAAAATCATTAA
Found at i:220330 original size:19 final size:20
Alignment explanation
Indices: 220288--220331 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
220278 ATTTTTTTTT
* **
220288 TTTTTTTAAATCATTAATTT
1 TTTTTTAAAATCATTAATAA
220308 TTTTTTAAAAT-ATTAATAA
1 TTTTTTAAAATCATTAATAA
220327 TTTTT
1 TTTTT
220332 ATGTATGTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTTTAAAATCATTAATAA
Found at i:220330 original size:20 final size:20
Alignment explanation
Indices: 220287--220331 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
220277 GATTTTTTTT
* *
220287 TTTTTTTTAAATCATTAATT
1 TTTTTTTAAAATCATTAATA
220307 TTTTTTTAAAAT-ATTAATAA
1 TTTTTTTAAAATCATTAAT-A
220327 TTTTT
1 TTTTT
220332 ATGTATGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTTTTAAAATCATTAATA
Done.